[gmx-users] Error in system_inflate.gro coordinates does not match
nickname.mittu at gmail.com
Mon Jul 28 07:42:15 CEST 2014
i used editconf
editconf -f protein.gro -o protein_newbox.gro -box (membrane box
vectors) -center *x y z*
but in z axis i have been increased box size 10.0000 (previously it is
6.23910 6.17970 6.91950
this is the em.gro first minimization image
mixing of lipid and protein molecule
On Fri, Jul 25, 2014 at 7:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 7/24/14, 11:57 AM, RINU KHATTRI wrote:
>> hello everyone
>> thank you justin
>> i did the same
>> till minimization without the ligand it is in the lipid and center but i
>> edit the box size arbitrary i used x and y axis as present in popc but in
>> axis used 10.00000 so there is overlapping of protein and lipid i think
>> this can create problem
> I don't understand if there is a question or problem here. If something
> is wrong, provide the exact command(s) used and provide images of the
> undesirable output. Without that information, there's nothing that I or
> anyone else can do to help you.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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